Contacts of the strand formed by residues 134 - 138 (chain D) in PDB entry 3DC1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D GLY 4.4 1.4 - - - +
133D ASP* 1.3 77.1 - - - +
135D VAL* 1.3 65.0 + - - +
155D ASN* 4.0 16.2 - - - +
157D ILE* 4.2 19.3 - - + +
178D TRP* 3.9 14.6 - - - -
189D ASN* 2.6 45.5 + - - +
190D THR 4.6 2.8 + - - -
191D PRO* 3.1 18.1 - - + +
192D LYS* 2.8 32.6 + - - +
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 4.5 5.6 - - + -
133D ASP* 4.8 1.8 - - + +
134D ASN* 1.3 82.6 - - - +
136D LEU* 1.3 65.3 + - - +
137D LEU* 4.1 0.6 + - + -
149D LEU* 4.8 4.0 - - + -
154D CYS* 4.0 22.2 - - + -
155D ASN 3.4 14.9 + - - +
156D ILE* 3.7 24.2 - - + -
157D ILE* 2.9 30.8 + - - +
192D LYS* 4.9 2.5 - - + -
193D PHE* 3.3 51.4 - - + -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D VAL* 1.3 77.9 - - - +
137D LEU* 1.3 59.9 + - - +
157D ILE* 3.5 22.2 - - + +
159D VAL* 4.1 11.4 - - + -
171D LEU* 4.3 9.4 - - + -
174D ILE* 3.9 28.0 - - + -
175D LEU* 4.3 2.7 - - + -
191D PRO* 3.4 37.7 - - + -
193D PHE* 2.9 16.6 + - - +
194D LEU* 3.4 14.6 - - + +
195D TYR* 2.6 35.2 + - - +
225D PHE* 4.1 26.2 - - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D VAL* 4.1 1.7 + - + -
136D LEU* 1.3 73.2 - - - +
138D ASP* 1.3 61.9 + - - +
139D GLU* 4.0 12.6 - - + -
141D ALA* 3.5 28.5 - - + -
145D THR* 4.7 1.8 - - + -
146D LEU* 4.2 9.4 - - + -
149D LEU* 3.8 26.9 - - + -
156D ILE* 3.8 19.2 - - + +
157D ILE 3.4 4.6 + - - -
158D ASN* 3.2 8.8 - - - +
159D VAL* 2.7 34.2 + - - -
166D ILE* 5.4 0.4 - - - -
193D PHE* 6.1 0.2 - - + -
194D LEU* 4.9 2.0 - - - -
195D TYR* 3.2 46.7 - - + +
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 1.3 77.0 - - - +
139D GLU* 1.3 59.4 + - - +
140D PRO 2.9 21.7 - - - +
141D ALA* 3.5 10.0 + - - +
159D VAL 3.4 16.2 - - - +
161D SER* 3.8 23.3 + - - -
165D GLY* 4.7 3.6 - - - -
166D ILE* 3.1 31.5 + - + +
195D TYR 4.0 1.7 - - - +
196D THR* 3.0 29.4 + - - -
197D VAL 5.6 0.2 - - - +
201D ASN* 4.6 9.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il